Abstract B060: Characterization of DNA repair defects in CDK12 mutant prostate cancer and the identification of differential vulnerabilities
Authors: Sander Frank, Ilsa Coleman, Navonil De Sarkar, Dmytro Rudoy, Valeri Vasioukhin, Pete Nelson
Journal: Cancer Research (2023)

Abstract Background: CDK12 expression is lost in ~5% of metastatic castration-resistant prostate cancer (mCRPC) and associates with aggressive disease. Previous literature, based on acute CDK12-loss models, proposes a mechanism where CDK12 loss leads to a homologous recombination deficiency (HRD) phenotype via premature intronic polyadenylation of classic HR pathway genes, including BRCA1 and BRCA2. Cyclin K is an essential gene and functions in a heterodimer with CDK12 or CDK13. We sought to test if CDK12 loss: (1) confers HRD and a corresponding sensitivity to platinum and poly-ADP ribose polymerase (PARP) inhibitors and/or (2) confers synthetic lethality to other cellular targets and pathways. Methods: To investigate the role of CDK12 loss we used a combination of acute (Tet-inducible shRNA, CDK12/13 inhibitors) and adapted (naturally mutant LuCaP 189.4, CRISPR KO clones) models. DNA repair gene expression and polyadenylation site usage was measured by RNA-seq, qPCR, and western blot while HR function was measured by immunofluorescence for RAD51 foci following irradiation. Stable CDK12-negative (CDK12-neg) cell lines were treated with sgRNAs, PARP inhibitors, carboplatin, and CDK inhibitors to test for potential targeted vulnerabilities. Results: Acute CDK12 inhibition (6h, SR4835) confirmed the reported mechanism of 3’ transcript loss, but the effects were minimal in long term shCDK12 or CRISRP KO lines as measured by RNA-seq, qPCR, and western blot. CDK12-neg lines showed slight decreases in ATR and ATM protein but minimal changes in BRCA1 or BRCA2 and no decrease in RAD51 foci formation. Furthermore, these lines did not show increased sensitivity to carboplatin and only partial sensitivity to PARPi. Human tumor data were analyzed and showed that CDK12-neg tumors lack genomic signatures of HRD and do not show significant de-enrichment of long genes. However, CDK12-neg cell lines did show sensitivity to CDK13 KO or pharmacologic inhibition with CDK12/13 inhibitors (SR4835, THZ531, dinaciclib). In vivo treatment of LuCaP xenograft lines showed that 189.4 responded to SR4835, while two CDK12-intact lines (35 and 136) did not. Conclusions: Our data support a model where HRD is primarily a result of acute CDK12 loss, while the downregulation of long DNA repair genes is largely compensated for (via currently unknown mechanisms) in cells that have adapted to CDK12 loss. We suspect that the partial PARPi sensitivity observed in CDK12-neg lines is due to other (non-HRD) DNA repair deficiencies and potential mechanisms are under investigation. CDK12-neg cells exhibited dependency on CDK13, which can be targeted with semi-selective pharmacologic compounds, though our data support the development of specific CDK13 inhibitors to maximize synthetic lethality and minimize off-target effects. Finally, additional work is ongoing with CRISPR and drug screens to identify additional vulnerabilities in adapted CDK12-neg models and provide future clinical targets for this aggressive subset of mCRPC. Citation Format: Sander Frank, Ilsa Coleman, Navonil De Sarkar, Dmytro Rudoy, Valeri Vasioukhin, Pete Nelson. Characterization of DNA repair defects in CDK12 mutant prostate cancer and the identification of differential vulnerabilities [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B060.